In this article, the authors explore how the coffee processing method can influence coffee cup taste by evaluating three commercial coffee processing methods—full-washed, wet-hulled and pulped-natural—in use in the Indonesian specialty coffee origin of “Bajawa” on the island of Flores. Specifically, the research attempts to determine whether pulped-natural processing creates inherently lower quality coffee, while at the same time considering the environmental, resource and financial constraints of the Flores farm system. Sixty-seven coffee tasters in Australia, Indonesia and the USA tested composite samples by using blind cupping, comparative preference testing methodology. The results show a clear preference for pulped-natural processing (often considered an inferior method in Indonesia), indicating that processing method does influence coffee cup taste. The demonstrated quality results, coupled with low water use, low waste output and minimal processing equipment requirement indicates that pulped-natural processing in the Flores coffee industry warrants further investigation. This research also highlights the importance of considering traditional practices and local conditions along with market requirements when making recommendations for coffee value adding and quality improvement.